Niftyreg (is there other option in the reg_aladin that generates parameters' to be used in the Reg_resample?)

1

HI everyone.

I used the niftyreg reigstraiton method with this command:

reg_aladin -ref $REF_IMG -flo ${file} -res "${OUTPUT_DIR}/$(basename ${file%.*.*})_affine.nii.gz" -aff "${OUTPUT_DIR}/$(basename ${file%.*.*})_affine.txt" -ln 3 -maxit 1000

So the registered output is generated based on the code

ep2d_perf_p2_4mm-0002_affine_masked.nii.gz  ep2d_perf_p2_4mm-0002.nii_affine.txt
  ep2d_perf_p2_4mm-0002.nii_affine.nii.gz

And I want to use the registration parameters to my rest of imaging. So i used the txt file with the command using Reg_resample(Reg resample - CMIC). And this is the code

 # Apply transformation
reg_resample -ref $REF_IMG -flo $perf_file -trans $TRANSFORM_FILE -res $OUT_IMG

However, the reg_resample command doesn’t seem to accept the txt files. In this case, which format is needed? Or is there other option in the reg_aladin that generates parameters’ to be used in the Reg_resample?

Thank you!

2

it was the version issue i used for the niftyreg. I found that I was using niftyreg_v1.5.43. So it worked after I used the nifty_reg-1.3.9 version in a cluster.